We examined food combinations in relation to the quality of the overall diet and individual meals using a newly developed food combination questionnaire (FCQ) in a nationwide sample of Japanese adults aged 19-80 years ( = 2233). The quality of the overall diet and of each meal was assessed by the Healthy Eating Index-2015 (HEI-2015) and Nutrient-Rich Food Index 9.3 (NRF9.3). For all main meals (breakfast, lunch, and dinner), the most commonly consumed food combinations consisted of 'rice, total vegetables, and tea and coffee'. Consistently positive associations between these food combinations and diet quality were found for breakfast (Spearman r: ≥0.46). Positive rather weak associations between these food combinations and diet quality were also observed for lunch (Spearman r: ≤0.48). Conversely, the associations were inconsistent for dinner: inverse associations with HEI-2015 (Spearman r: ≤-0.35) and generally weak positive associations with NRF9.3 (Spearman r: ≥0.09). For snacks, the most commonly consumed food combinations consisted of 'confectioneries and tea and coffee', but these showed rather weak associations with diet quality. Similar results were obtained when associations with the quality of overall diet were investigated. The FCQ may be useful in capturing the complex nature of food combinations in Japanese adults.